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Genetic similarities between Cyclospora cayetanensis and cecum-infecting avian Eimeria spp. in apicoplast and mitochondrial genomes.

Tang K, Guo Y, Zhang L, Rowe LA, Roellig DM, Frace MA, Li N, Liu S, Feng Y, Xiao L - Parasit Vectors (2015)

Bottom Line: The assembled genomes of the apicoplast and mitochondrion were retrieved, annotated, and compared with reference genomes for other apicomplexans to infer genome organizations and phylogenetic relationships.Eight single-nucleotide and one 7-bp multiple-nucleotide variants were detected between the mitochondrial genomes of C. cayetanensis from this and recent studies.The apicoplast and mitochondrial genomes of C. cayetanensis are highly similar to those of cecum-infecting avian Eimeria spp. in both genome organization and sequences.

View Article: PubMed Central - PubMed

Affiliation: Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA. kht7@cdc.gov.

ABSTRACT

Background: Cyclospora cayetanensis is an important cause for diarrhea in children in developing countries and foodborne outbreaks of cyclosporiasis in industrialized nations. To improve understanding of the basic biology of Cyclospora spp. and development of molecular diagnostic tools and therapeutics, we sequenced the complete apicoplast and mitochondrial genomes of C. cayetanensis.

Methods: The genome of one Chinese C. cayetanensis isolate was sequenced using Roche 454 and Illumina technologies. The assembled genomes of the apicoplast and mitochondrion were retrieved, annotated, and compared with reference genomes for other apicomplexans to infer genome organizations and phylogenetic relationships. Sequence variations in the mitochondrial genome were identified by comparison of two C. cayetanensis nucleotide sequences from this study and a recent publication.

Results: The apicoplast and mitochondrial genomes of C. cayetanensis are 34,155 and 6,229 bp in size and code for 65 and 5 genes, respectively. Comparative genomic analysis showed high similarities between C. cayetanensis and Eimeria tenella in both genomes; they have 85.6% and 90.4% nucleotide sequence similarities, respectively, and complete synteny in gene organization. Phylogenetic analysis of the genomic sequences confirmed the genetic similarities between cecum-infecting avian Eimeria spp. and C. cayetanensis. Like in other coccidia, both genomes of C. cayetanensis are transcribed bi-directionally. The apicoplast genome is circular, codes for the complete machinery for protein biosynthesis, and contains two inverted repeats that differ slightly in LSU rRNA gene sequences. In contrast, the mitochondrial genome has a linear concatemer or circular mapping topology. Eight single-nucleotide and one 7-bp multiple-nucleotide variants were detected between the mitochondrial genomes of C. cayetanensis from this and recent studies.

Conclusions: The apicoplast and mitochondrial genomes of C. cayetanensis are highly similar to those of cecum-infecting avian Eimeria spp. in both genome organization and sequences. The availability of sequence data beyond rRNA and heat shock protein genes could facilitate studies of C. cayetanensis biology and development of genotyping tools for investigations of cyclosporiasis outbreaks.

No MeSH data available.


Related in: MedlinePlus

Synteny in gene organizations between Cyclospora cayetanensis and Eimeria spp. in the apicoplast (a) and mitochondrial (b) genomes. The color blocks are conserved segments of sequences internally free from genome rearrangements, whereas the inverted white peaks within each block are sequence divergence between the C. cayetanensis genome and other genomes under analysis
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Fig3: Synteny in gene organizations between Cyclospora cayetanensis and Eimeria spp. in the apicoplast (a) and mitochondrial (b) genomes. The color blocks are conserved segments of sequences internally free from genome rearrangements, whereas the inverted white peaks within each block are sequence divergence between the C. cayetanensis genome and other genomes under analysis

Mentions: A Blast search of the NCBI database with the C. cayetanensis apicoplast sequence showed that the sequence was most similar to the apicoplast genome of E. tenella (access no. AY217738.1). Genome sequence alignments showed that the C. cayetanensis apicoplast genome has complete gene synteny to the apicoplast genome of E. tenella and other Eimeria spp. and good synteny to the genome of T. gondii (Fig. 3a). Aligning the assembled apicoplast genome sequence to that of the E. tenella apicoplast genome with NUCmer resulted in a single alignment that covers 99.85 % of the apicoplast genome, confirming the synteny between the two genomes. The identity between the two genomes in the aligned regions was 85.6 %. The sequence divergence between the two genomes was mostly 8–10 % as calculated in a sliding window of 1,000 bp in sequence read mapping. However, much lower sequence differences were seen in rRNA genes within the two IR units (Fig. 4a). SNV analysis by read mapping did not identify any intra-isolate sequence polymorphism beyond what was described between the two IRs.Fig. 3


Genetic similarities between Cyclospora cayetanensis and cecum-infecting avian Eimeria spp. in apicoplast and mitochondrial genomes.

Tang K, Guo Y, Zhang L, Rowe LA, Roellig DM, Frace MA, Li N, Liu S, Feng Y, Xiao L - Parasit Vectors (2015)

Synteny in gene organizations between Cyclospora cayetanensis and Eimeria spp. in the apicoplast (a) and mitochondrial (b) genomes. The color blocks are conserved segments of sequences internally free from genome rearrangements, whereas the inverted white peaks within each block are sequence divergence between the C. cayetanensis genome and other genomes under analysis
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4495940&req=5

Fig3: Synteny in gene organizations between Cyclospora cayetanensis and Eimeria spp. in the apicoplast (a) and mitochondrial (b) genomes. The color blocks are conserved segments of sequences internally free from genome rearrangements, whereas the inverted white peaks within each block are sequence divergence between the C. cayetanensis genome and other genomes under analysis
Mentions: A Blast search of the NCBI database with the C. cayetanensis apicoplast sequence showed that the sequence was most similar to the apicoplast genome of E. tenella (access no. AY217738.1). Genome sequence alignments showed that the C. cayetanensis apicoplast genome has complete gene synteny to the apicoplast genome of E. tenella and other Eimeria spp. and good synteny to the genome of T. gondii (Fig. 3a). Aligning the assembled apicoplast genome sequence to that of the E. tenella apicoplast genome with NUCmer resulted in a single alignment that covers 99.85 % of the apicoplast genome, confirming the synteny between the two genomes. The identity between the two genomes in the aligned regions was 85.6 %. The sequence divergence between the two genomes was mostly 8–10 % as calculated in a sliding window of 1,000 bp in sequence read mapping. However, much lower sequence differences were seen in rRNA genes within the two IR units (Fig. 4a). SNV analysis by read mapping did not identify any intra-isolate sequence polymorphism beyond what was described between the two IRs.Fig. 3

Bottom Line: The assembled genomes of the apicoplast and mitochondrion were retrieved, annotated, and compared with reference genomes for other apicomplexans to infer genome organizations and phylogenetic relationships.Eight single-nucleotide and one 7-bp multiple-nucleotide variants were detected between the mitochondrial genomes of C. cayetanensis from this and recent studies.The apicoplast and mitochondrial genomes of C. cayetanensis are highly similar to those of cecum-infecting avian Eimeria spp. in both genome organization and sequences.

View Article: PubMed Central - PubMed

Affiliation: Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA. kht7@cdc.gov.

ABSTRACT

Background: Cyclospora cayetanensis is an important cause for diarrhea in children in developing countries and foodborne outbreaks of cyclosporiasis in industrialized nations. To improve understanding of the basic biology of Cyclospora spp. and development of molecular diagnostic tools and therapeutics, we sequenced the complete apicoplast and mitochondrial genomes of C. cayetanensis.

Methods: The genome of one Chinese C. cayetanensis isolate was sequenced using Roche 454 and Illumina technologies. The assembled genomes of the apicoplast and mitochondrion were retrieved, annotated, and compared with reference genomes for other apicomplexans to infer genome organizations and phylogenetic relationships. Sequence variations in the mitochondrial genome were identified by comparison of two C. cayetanensis nucleotide sequences from this study and a recent publication.

Results: The apicoplast and mitochondrial genomes of C. cayetanensis are 34,155 and 6,229 bp in size and code for 65 and 5 genes, respectively. Comparative genomic analysis showed high similarities between C. cayetanensis and Eimeria tenella in both genomes; they have 85.6% and 90.4% nucleotide sequence similarities, respectively, and complete synteny in gene organization. Phylogenetic analysis of the genomic sequences confirmed the genetic similarities between cecum-infecting avian Eimeria spp. and C. cayetanensis. Like in other coccidia, both genomes of C. cayetanensis are transcribed bi-directionally. The apicoplast genome is circular, codes for the complete machinery for protein biosynthesis, and contains two inverted repeats that differ slightly in LSU rRNA gene sequences. In contrast, the mitochondrial genome has a linear concatemer or circular mapping topology. Eight single-nucleotide and one 7-bp multiple-nucleotide variants were detected between the mitochondrial genomes of C. cayetanensis from this and recent studies.

Conclusions: The apicoplast and mitochondrial genomes of C. cayetanensis are highly similar to those of cecum-infecting avian Eimeria spp. in both genome organization and sequences. The availability of sequence data beyond rRNA and heat shock protein genes could facilitate studies of C. cayetanensis biology and development of genotyping tools for investigations of cyclosporiasis outbreaks.

No MeSH data available.


Related in: MedlinePlus